Remove sqlalchemy create_all() call

Let alembic handle the database creation and migration

Makefile

-.PHONY: help build tag push refresh release db initdb test db_image test_image
+.PHONY: help build tag push refresh release db init_db upgrade_db test db_image test_image
 
 OWNER := registry.esss.lu.se/ics-infrastructure
 GIT_TAG := $(shell git describe --always)
@@ -40,8 +40,12 @@ release: ## build, tag, and push all stacks
 db: ## start postgres and redis for development
 	docker-compose up -d postgres redis
 
-initdb: ## initialize the dev database
-	docker-compose run --rm web flask initdb
+init_db: ## initialize the dev database
+	docker-compose run --rm web flask db upgrade head
+	docker-compose run --rm web flask create_defaults
+
+upgrade_db: ## upgrade the dev database
+	docker-compose run --rm web flask db upgrade head
 
 test:  ## run the tests (on current directory)
 	docker-compose run --rm web pytest --cov=app -v

README.rst

@@ -19,9 +19,10 @@ You can use docker for development:
     or
     $ make db
     # Initialize the database
-    $ docker-compose run --rm web flask initdb
+    $ docker-compose run --rm web flask db upgrade head
+    $ docker-compose run --rm web flask create_defaults
     or
-    $ make initdb
+    $ make init_db
 
 3. Start the application::
 

app/commands.py

@@ -63,10 +63,8 @@ def sync_users():
 
 def register_cli(app):
     @app.cli.command()
-    def initdb():
-        """Create the database tables and initialize them with default values"""
-        db.engine.execute('CREATE EXTENSION IF NOT EXISTS citext')
-        db.create_all()
+    def create_defaults():
+        """Create the database default values"""
         for instance in defaults:
             db.session.add(instance)
             try: